Does anybody know an opensource software package for whole genome assembly of cDNA with Illumina paired-end sequencing? I'm really looking for an assembler designed for cDNA data, not DNA. I don't think that programs like Velvet or SSAKE can deal with this kind of data (I may be wrong). MIRA seems OK but it is not quite clear whether it takes the "paired-end" feature into account when assembling cDNA data. Any help is much appreciated !!

I don't understand your question - cDNA is just a small part of a whole genome. Are you talking about an EST assembly of the transcriptome (i.e. extract mRNA, covert to cDNA, sequence it, assemble it).

Thx Zigster. Yes I mean the transcriptome assembly. After some research, it seems that MIRA can deal with this kind of data (EST + paired end + short read). I saw in several papers that CAP3 was used on the assembled contigs (to get larger contigs). Is this a good idea ? Do you have any advice ?